2023
Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome
Rahman S, Dong P, Apontes P, Fernando M, Kosoy R, Townsley K, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos S, Brennand K, Fullard J, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Research 2023, 51: 11142-11161. PMID: 37811875, PMCID: PMC10639075, DOI: 10.1093/nar/gkad798.Peer-Reviewed Original ResearchConceptsChromatin interactomeNeural developmentSpecific gene expressionEnhancer-promoter loopsDistinct cell typesGenome compartmentalizationRepressive compartmentGenome architectureFine-scale changesGenome structureChromatin loopsGWAS lociTAD boundariesTranscriptional inactivationActive promotersGene expressionInteractomeGenomeCell typesComplex organDisease mechanismsHuman brainAdult prefrontal cortexAdult human brainNeurodevelopmental processes
2022
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling
Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling. Molecular & Cellular Proteomics 2022, 21: 100422. PMID: 36198386, PMCID: PMC9650050, DOI: 10.1016/j.mcpro.2022.100422.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProximity labelingBiological functionsComplex protein-protein interactionsProximity labeling methodProtein-DNA interactionsCell-cell communicationMost biological functionsDistinct cell typesProtein-RNANerve cell functionCell typesBiomolecular complexesCellular levelPhysical interactionProteomeCell functionSpecific subsetProteinSynaptic plasticityComplete catalogLabeling methodRecent advancesPowerful toolAxonal projectionsMicroenvironmental sensing by fibroblasts controls macrophage population size
Zhou X, Franklin RA, Adler M, Carter TS, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, Medzhitov R. Microenvironmental sensing by fibroblasts controls macrophage population size. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2205360119. PMID: 35930670, PMCID: PMC9371703, DOI: 10.1073/pnas.2205360119.Peer-Reviewed Original ResearchConceptsCell typesDensity-dependent gene expressionTGF-β target genesDiverse cell typesActin-dependent mechanismLineage-specific growth factorsDistinct cell typesGrowth factor availabilityActivation of YAP1Different cell typesExpression programsMicroenvironmental sensingTranscriptional coactivatorTarget genesGene expressionPopulation sizeFactor availabilityPopulation numbersTissue environmentTissue integrityHippoProliferation of macrophagesYAP1Animal tissuesMechanical forces
2018
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw C, Pardiñas AF, Hu M, Jin F, Li Y, Owen M, O’Donovan M, Walters J, Posthuma D, Reimers M, Levitt P, Weinberger D, Hyde T, Kleinman J, Geschwind D, Hawrylycz M, State M, Sanders S, Sullivan P, Gerstein M, Lein E, Knowles J, Sestan N, Willsey A, Oldre A, Szafer A, Camarena A, Cherskov A, Charney A, Abyzov A, Kozlenkov A, Safi A, Jones A, Ashley-Koch A, Ebbert A, Price A, Sekijima A, Kefi A, Bernard A, Amiri A, Sboner A, Clark A, Jaffe A, Tebbenkamp A, Sodt A, Guillozet-Bongaarts A, Nairn A, Carey A, Huttner A, Chervenak A, Szekely A, Shieh A, Harmanci A, Lipska B, Carlyle B, Gregor B, Kassim B, Sheppard B, Bichsel C, Hahn C, Lee C, Chen C, Kuan C, Dang C, Lau C, Cuhaciyan C, Armoskus C, Mason C, Liu C, Slaughterbeck C, Bennet C, Pinto D, Polioudakis D, Franjic D, Miller D, Bertagnolli D, Lewis D, Feng D, Sandman D, Clarke D, Williams D, DelValle D, Fitzgerald D, Shen E, Flatow E, Zharovsky E, Burke E, Olson E, Fulfs E, Mattei E, Hadjimichael E, Deelman E, Navarro F, Wu F, Lee F, Cheng F, Goes F, Vaccarino F, Liu F, Hoffman G, Gürsoy G, Gee G, Mehta G, Coppola G, Giase G, Sedmak G, Johnson G, Wray G, Crawford G, Gu G, van Bakel H, Witt H, Yoon H, Pratt H, Zhao H, Glass I, Huey J, Arnold J, Noonan J, Bendl J, Jochim J, Goldy J, Herstein J, Wiseman J, Miller J, Mariani J, Stoll J, Moore J, Szatkiewicz J, Leng J, Zhang J, Parente J, Rozowsky J, Fullard J, Hohmann J, Morris J, Phillips J, Warrell J, Shin J, An J, Belmont J, Nyhus J, Pendergraft J, Bryois J, Roll K, Grennan K, Aiona K, White K, Aldinger K, Smith K, Girdhar K, Brouner K, Mangravite L, Brown L, Collado-Torres L, Cheng L, Gourley L, Song L, Ubieta L, Habegger L, Ng L, Hauberg M, Onorati M, Webster M, Kundakovic M, Skarica M, Reimers M, Johnson M, Chen M, Garrett M, Sarreal M, Reding M, Gu M, Peters M, Fisher M, Gandal M, Purcaro M, Smith M, Brown M, Shibata M, Brown M, Xu M, Yang M, Ray M, Shapovalova N, Francoeur N, Sjoquist N, Mastan N, Kaur N, Parikshak N, Mosqueda N, Ngo N, Dee N, Ivanov N, Devillers O, Roussos P, Parker P, Manser P, Wohnoutka P, Farnham P, Zandi P, Emani P, Dalley R, Mayani R, Tao R, Gittin R, Straub R, Lifton R, Jacobov R, Howard R, Park R, Dai R, Abramowicz S, Akbarian S, Schreiner S, Ma S, Parry S, Shapouri S, Weissman S, Caldejon S, Mane S, Ding S, Scuderi S, Dracheva S, Butler S, Lisgo S, Rhie S, Lindsay S, Datta S, Souaiaia T, Roychowdhury T, Gomez T, Naluai-Cecchini T, Beach T, Goodman T, Gao T, Dolbeare T, Fliss T, Reddy T, Chen T, Hyde T, Brunetti T, Lemon T, Desta T, Borrman T, Haroutunian V, Spitsyna V, Swarup V, Shi X, Jiang Y, Xia Y, Chen Y, Jiang Y, Wang Y, Chae Y, Yang Y, Kim Y, Riley Z, Krsnik Z, Deng Z, Weng Z, Lin Z, Li Z. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 2018, 362 PMID: 30545854, PMCID: PMC6413317, DOI: 10.1126/science.aat7615.Peer-Reviewed Original ResearchConceptsIntegrative functional genomic analysisFunctional genomic analysisCell typesGene coexpression modulesDistinct cell typesCell type-specific dynamicsGenomic basisEpigenomic reorganizationEpigenomic landscapeEpigenomic regulationGenomic analysisCoexpression modulesIntegrative analysisHuman brain developmentFetal transitionHuman neurodevelopmentGenetic associationCellular compositionNeuropsychiatric riskBrain developmentNeurodevelopmental processesGenesTraitsPostnatal developmentNeuropsychiatric disorders
2017
Molecular and cellular reorganization of neural circuits in the human lineage
Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Molecular and cellular reorganization of neural circuits in the human lineage. Science 2017, 358: 1027-1032. PMID: 29170230, PMCID: PMC5776074, DOI: 10.1126/science.aan3456.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic dataDistinct functional categoriesDistinct cell typesBiosynthesis genesTranscriptome sequencingHuman lineageTranscriptomic dataFunctional categoriesCellular reorganizationExpression differencesPhylogenetic reorganizationFunctional analysisCell typesGenesCellular featuresCellular differencesHuman specificityNeural circuitsLineagesMultiple levelsReorganizationSequencingHumansChimpanzeesAdult humans
2015
Fibronectin signals through integrin α5β1 to regulate cardiovascular development in a cell type-specific manner
Chen D, Wang X, Liang D, Gordon J, Mittal A, Manley N, Degenhardt K, Astrof S. Fibronectin signals through integrin α5β1 to regulate cardiovascular development in a cell type-specific manner. Developmental Biology 2015, 407: 195-210. PMID: 26434918, PMCID: PMC5312697, DOI: 10.1016/j.ydbio.2015.09.016.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornBranchial RegionCardiovascular SystemCell LineageEmbryo, MammalianFemaleFibronectinsIntegrin alpha5beta1LIM-Homeodomain ProteinsMice, KnockoutModels, BiologicalMorphogenesisMutationNeural CrestOrgan SpecificityPharynxPhenotypePregnancySignal TransductionStem CellsT-Box Domain ProteinsThymus GlandTranscription FactorsConceptsPharyngeal arch arteriesCardiovascular developmentIntegrin α5Pharyngeal arch mesodermCell type-specific mannerCell typesMid-gestation lethalityType-specific mannerDistinct cell typesCardiac outflow tractMorphogenetic defectsPharyngeal regionMouse embryogenesisConditional mutantsExtracellular matrix glycoproteinEmbryonic developmentMutagenesis studiesCardiovascular morphogenesisNeural crestPAA formationSurface ectodermDefective formationArch arteriesFN1Matrix glycoprotein
2014
SP0104 The Molecular Basis of Autoimmune Disease
Hafler D. SP0104 The Molecular Basis of Autoimmune Disease. Annals Of The Rheumatic Diseases 2014, 73: 27-28. DOI: 10.1136/annrheumdis-2014-eular.6254.Peer-Reviewed Original ResearchGenome-wide association studiesNon-coding regionsConsensus transcription factorNumerous genetic associationsDistinct cell typesDifferent autoimmune diseasesAutoimmune diseasesChromatin mapsTh17 cellsGWAS hitsHigh NaCl levelsTranscription factorsDNA sequencesMolecular basisGenetic dataCausal mutationsDisease riskAssociation studiesMechanistic basisCommon SNPsNucleotide variantsAP-1Risk SNPsCell typesSpecific disruption
2012
Intrinsic properties and functional circuitry of the AII amacrine cell
DEMB JB, SINGER JH. Intrinsic properties and functional circuitry of the AII amacrine cell. Visual Neuroscience 2012, 29: 51-60. PMID: 22310372, PMCID: PMC3561778, DOI: 10.1017/s0952523811000368.Peer-Reviewed Original ResearchConceptsAII amacrine cellsAmacrine cellsPhotopic conditionsOFF ganglion cellsRod amacrine cellsCone bipolar cellsGanglion cell typesCone-mediated visionRod-mediated visionAII networkCell typesGanglion cellsRetinal neuronsExcitatory interneuronsBipolar cellsMammalian retinaFunctional circuitryAIIDistinct cell typesOutput neuronsNeuronsInhibition pathwayMotion sensitivityPhotoreceptor pathwaysCells
2009
Role of Scrib and Dlg in anterior-posterior patterning of the follicular epithelium during Drosophila oogenesis
Li Q, Shen L, Xin T, Xiang W, Chen W, Gao Y, Zhu M, Yu L, Li M. Role of Scrib and Dlg in anterior-posterior patterning of the follicular epithelium during Drosophila oogenesis. BMC Developmental Biology 2009, 9: 60. PMID: 19948068, PMCID: PMC2810132, DOI: 10.1186/1471-213x-9-60.Peer-Reviewed Original ResearchConceptsTumor suppressor geneDlg functionFate inductionPosterior patterningCell fateEgg chambersDrosophila tumor suppressor geneSuppressor geneBorder cell fateFollicle cellsCell fate inductionAnterior-posterior patterningDrosophila egg developmentRole of ScribFollicle cell epitheliumFurther genetic analysisMultiple signaling pathwaysDistinct cell typesAnterior-posterior axisDrosophila oogenesisEpithelial polarityEpithelial patterningMosaic clonesFollicular epitheliumAnterior domain
2006
A low diversity of ANTP class homeobox genes in Placozoa
Monteiro A, Schierwater B, Dellaporta S, Holland P. A low diversity of ANTP class homeobox genes in Placozoa. Evolution & Development 2006, 8: 174-182. PMID: 16509895, DOI: 10.1111/j.1525-142x.2006.00087.x.Peer-Reviewed Original ResearchConceptsANTP class genesClass genesGene familyHomeobox genesLow diversityANTP class homeobox genesTight gene clusterClass homeobox genesDistinct cell typesPRD classBilaterian animalsTrichoplax adhaerensGene clusterBody patterningBody organizationMarine animalsTrichoplaxExtensive screenGenesCell typesMetazoansLarge diversitySitu hybridizationDiversityFamilyAssociation between pathways in regulatory networks
Kluger Y, Kluger H, Tuck D. Association between pathways in regulatory networks. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2006, 2006: 2036-2040. PMID: 17946929, DOI: 10.1109/iembs.2006.260730.Peer-Reviewed Original ResearchConceptsRegulatory networksCo-regulated pathwaysHuman regulatory networkRegulatory network connectivityDistinct cell typesTranscriptional regulatory levelCondition-specific networksGene regulationIndividual genesCell statesTranscriptional activityCell typesCell progressionExpression signaturesNumerous pathwaysGene profilesRemarkable connectivityMultiple pathwaysPathwayGenesRegulatory levelsRegulationExpressionCellsNotable differences
1989
Amino-terminal sequences of prosomatostatin direct intracellular targeting but not processing specificity
Sevarino K, Stork P, Ventimiglia R, Mandel G, Goodman R. Amino-terminal sequences of prosomatostatin direct intracellular targeting but not processing specificity. Cell 1989, 57: 11-19. PMID: 2564811, DOI: 10.1016/0092-8674(89)90167-0.Peer-Reviewed Original ResearchConceptsEndocrine cell linesRat preprosomatostatinCarboxy-terminal thirdDistinct cell typesAmino-terminal sequenceCell linesHybrid proteinLeader sequenceIntracellular targetingRegulated pathwayPreprosomatostatin 1Cellular factorsExpression vectorCell typesPattern of processingProcessing siteBioactive peptidesAnglerfish isletsSequenceDifferential processingPeptidesProteinResiduesPathwayHigh levels
1973
Graft-vs-host reactivity of mouse thymocytes: effect of cortisone pretreatment of donors.
Tigelaar R, Asofsky R. Graft-vs-host reactivity of mouse thymocytes: effect of cortisone pretreatment of donors. The Journal Of Immunology 1973, 110: 567-74. PMID: 4405321, DOI: 10.4049/jimmunol.110.2.567.Peer-Reviewed Original ResearchConceptsSpleen weightNormal thymocytesPeripheral lymph node cellsCell-mediated immune reactionsBALB/c miceLymph node cellsThymus-derived cellsCortisone-resistant thymocytesLymphoid cell populationsCortisone pretreatmentGVH reactivityHost reactivityC miceNode cellsNormal donorsImmune reactionsThymus cellsCortisone acetateCumulative mortalityThymocytesMortalityUnique populationCell populationsMouse thymocytesDistinct cell types
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply